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Better consistency in using snake_case
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tverbeiren committed Feb 13, 2024
1 parent e68a038 commit b2d3914
Showing 2 changed files with 17 additions and 17 deletions.
18 changes: 9 additions & 9 deletions src/cutadapt/config.vsh.yaml
Original file line number Diff line number Diff line change
@@ -83,7 +83,7 @@ functionality:
####################################################################
- name: Specify Adapters for R2
arguments:
- name: --adapterR2
- name: --adapter_r2
alternatives: [-A]
type: string
multiple: true
@@ -93,7 +93,7 @@ functionality:
trimmed. If a '$' character is appended ('anchoring'), the
adapter is only found if it is a suffix of the read.
required: false
- name: --frontR2
- name: --front_r2
alternatives: [-G]
type: string
multiple: true
@@ -104,7 +104,7 @@ functionality:
a '^' character is prepended ('anchoring'), the adapter is
only found if it is a prefix of the read.
required: false
- name: --anywhereR2
- name: --anywhere_r2
alternatives: [-B]
type: string
multiple: true
@@ -121,15 +121,15 @@ functionality:
####################################################################
- name: Specify Adapters using Fasta files for R2
arguments:
- name: --adapterR2_fasta
- name: --adapter_r2_fasta
type: file
description: |
Fasta file containing sequences of an adapter ligated to the 3' end (paired data:
of the first read). The adapter and subsequent bases are
trimmed. If a '$' character is appended ('anchoring'), the
adapter is only found if it is a suffix of the read.
required: false
- name: --frontR2_fasta
- name: --front_r2_fasta
type: file
description: |
Fasta file containing sequences of an adapter ligated to the 5' end (paired data:
@@ -138,7 +138,7 @@ functionality:
a '^' character is prepended ('anchoring'), the adapter is
only found if it is a prefix of the read.
required: false
- name: --anywhereR2_fasta
- name: --anywhere_r2_fasta
type: file
description: |
Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'
@@ -242,12 +242,12 @@ functionality:
type: integer
multiple: true
description: |
Remove LEN bases from each read (or R1 if paired; use --cutR2
Remove LEN bases from each read (or R1 if paired; use --cut_r2
option for R2). If LEN is positive, remove bases from the
beginning. If LEN is negative, remove bases from the end.
Can be used twice if LENs have different signs. Applied
*before* adapter trimming.
- name: --cutR2
- name: --cut_r2
type: integer
multiple: true
description: |
@@ -269,7 +269,7 @@ functionality:
paired. If one value is given, only the 3' end is trimmed.
If two comma-separated cutoffs are given, the 5' end is
trimmed with the first cutoff, the 3' end with the second.
- name: --quality_cutoffR2
- name: --quality_cutoff_r2
alternatives: [-Q]
type: string
description: |
16 changes: 8 additions & 8 deletions src/cutadapt/script.sh
Original file line number Diff line number Diff line change
@@ -33,12 +33,12 @@ adapter_args=$(echo \
${par_front_fasta:+--front "file:${par_front_fasta}"} \
${par_anywhere:+--anywhere "${par_anywhere}"} \
${par_anywhere_fasta:+--anywhere "file:${par_anywhere_fasta}"} \
${par_adapterR2:+--adapterR2 "${par_adapterR2}"} \
${par_adapterR2_fasta:+--adapterR2 "file:${par_adapterR2_fasta}"} \
${par_frontR2:+--frontR2 "${par_frontR2}"} \
${par_frontR2_fasta:+--frontR2 "file:${par_frontR2_fasta}"} \
${par_anywhereR2:+--anywhereR2 "${par_anywhereR2}"} \
${par_anywhereR2_fasta:+--anywhereR2 "file:${par_anywhereR2_fasta}"}
${par_adapter_r2:+--adapter_r2 "${par_adapter_r2}"} \
${par_adapter_r2_fasta:+--adapter_r2 "file:${par_adapter_r2_fasta}"} \
${par_front_r2:+--front_r2 "${par_front_r2}"} \
${par_front_r2_fasta:+--front_r2 "file:${par_front_r2_fasta}"} \
${par_anywhere_r2:+--anywhere_r2 "${par_anywhere_r2}"} \
${par_anywhere_r2_fasta:+--anywhere_r2 "file:${par_anywhere_r2_fasta}"}
)
echo "Arguments to cutadapt:"
echo "$adapter_args"
@@ -90,10 +90,10 @@ echo ">> Parsing read modification arguments"

mod_args=$(echo \
${par_cut:+--cut "${par_cut}"} \
${par_cutR2:+--cutR2 "${par_cutR2}"} \
${par_cut_r2:+--cut_r2 "${par_cut_r2}"} \
${par_nextseq_trim:+--nextseq-trim "${par_nextseq_trim}"} \
${par_quality_cutoff:+--quality-cutoff "${par_quality_cutoff}"} \
${par_quality_cutoffR2:+--quality-cutoffR2 "${par_quality_cutoffR2}"} \
${par_quality_cutoff_r2:+--quality-cutoff_r2 "${par_quality_cutoff_r2}"} \
${par_quality_base:+--quality-base "${par_quality_base}"} \
${par_poly_a:+--poly-a} \
${par_length:+--length "${par_length}"} \

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